1
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Cabrera VM. New Canary Islands Roman mediated settlement hypothesis deduced from coalescence ages of curated maternal indigenous lineages. Sci Rep 2024; 14:11150. [PMID: 38750053 PMCID: PMC11096394 DOI: 10.1038/s41598-024-61731-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 05/09/2024] [Indexed: 05/18/2024] Open
Abstract
Numerous genetic studies have contributed to reconstructing the human history of the Canary Islands population. The recent use of new ancient DNA targeted enrichment and next-generation sequencing techniques on new Canary Islands samples have greatly improved these molecular results. However, the bulk of the available data is still provided by the classic mitochondrial DNA phylogenetic and phylogeographic studies carried out on the indigenous, historical, and extant human populations of the Canary Islands. In the present study, making use of all the accumulated mitochondrial information, the existence of DNA contamination and archaeological sample misidentification in those samples is evidenced. Following a thorough review of these cases, the new phylogeographic analysis revealed the existence of a heterogeneous indigenous Canarian population, asymmetrically distributed across the various islands, which most likely descended from a unique mainland settlement. These new results and new proposed coalescent ages are compatible with a Roman-mediated arrival driven by the exploitation of the purple dye manufacture in the Canary Islands.
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Affiliation(s)
- Vicente M Cabrera
- Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, 38200, San Cristobal de La Laguna, Spain.
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2
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Luis JR, Palencia-Madrid L, Mendoza VC, Garcia-Bertrand R, de Pancorbo MM, Herrera RJ. The Y chromosome of autochthonous Basque populations and the Bronze Age replacement. Sci Rep 2021; 11:5607. [PMID: 33692401 PMCID: PMC7970938 DOI: 10.1038/s41598-021-84915-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 02/19/2021] [Indexed: 11/09/2022] Open
Abstract
Here we report on the Y haplogroup and Y-STR diversity of the three autochthonous Basque populations of Alava (n = 54), Guipuzcoa (n = 30) and Vizcaya (n = 61). The same samples genotyped for Y-chromosome SNPs were typed for 17 Y-STR loci (DYS19, DYS385a/b, DYS398I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, Y-GATA H4) using the AmpFlSTR Yfiler system. Six major haplogroups (R, I, E, J, G, and DE) were detected, being R-S116 (P312) haplogroup the most abundant at 75.0% in Alava, 86.7% in Guipuzcoa and 87.3% in Vizcaya. Age estimates for the R-S116 mutation in the Basque Country are 3975 ± 303, 3680 ± 345 and 4553 ± 285 years for Alava, Guipuzcoa and Vizcaya, respectively. Pairwise Rst genetic distances demonstrated close Y-chromosome affinities among the three autochthonous Basque populations and between them and the male population of Ireland and Gascony. In a MDS plot, the population of Ireland segregates within the Basque cluster and closest to the population of Guipuzcoa, which plots closer to Ireland than to any of the other Basque populations. Overall, the results support the notion that during the Bronze Age a dispersal of individuals carrying the R-S116 mutation reached the Basque Country replacing the Paleolithic/Neolithic Y chromosome of the region.
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Affiliation(s)
- Javier Rodriguez Luis
- Area de Antropología, Facultad de Biología, Universidad de Santiago de Compostela, Campus Sur s/n, 15782, Santiago de Compostela, Spain
| | - Leire Palencia-Madrid
- BIOMICs Research Group, Dpto. Z. y Biologia Celular A., Lascaray Research Centre, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Vivian C Mendoza
- Department of Molecular Biology, Colorado College, Colorado Springs, CO, 80903, USA
| | | | - Marian M de Pancorbo
- BIOMICs Research Group, Dpto. Z. y Biologia Celular A., Lascaray Research Centre, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Rene J Herrera
- Department of Molecular Biology, Colorado College, Colorado Springs, CO, 80903, USA.
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3
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SCHMIDT RYANW, WAKABAYASHI KEN, WAKU DAISUKE, GAKUHARI TAKASHI, KOGANEBUCHI KAE, OGAWA MOTOYUKI, KARSTEN JORDANK, SOKHATSKY MYKHAILO, OOTA HIROKI. Analysis of ancient human mitochondrial DNA from Verteba Cave, Ukraine: insights into the Late Neolithic-Chalcolithic Cucuteni–Tripolye culture. ANTHROPOL SCI 2020. [DOI: 10.1537/ase.200205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- RYAN W. SCHMIDT
- Department of Anatomy, Kitasato University, Sagamihara
- School of Archaeology, Earth Institute, University College Dublin, Dublin
| | | | - DAISUKE WAKU
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo
| | - TAKASHI GAKUHARI
- Department of Anatomy, Kitasato University, Sagamihara
- Kanazawa University, Center for Cultural Resource Studies, Kanazawa
| | | | | | - JORDAN K. KARSTEN
- Department of Anthropology and Religious Studies, University of Wisconsin-Oshkosh, Oshkosh
| | | | - HIROKI OOTA
- Department of Anatomy, Kitasato University, Sagamihara
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo
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4
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Mitochondrial DNA, a Powerful Tool to Decipher Ancient Human Civilization from Domestication to Music, and to Uncover Historical Murder Cases. Cells 2019; 8:cells8050433. [PMID: 31075917 PMCID: PMC6562384 DOI: 10.3390/cells8050433] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/17/2019] [Accepted: 05/07/2019] [Indexed: 11/28/2022] Open
Abstract
Mitochondria are unique organelles carrying their own genetic material, independent from that in the nucleus. This review will discuss the nature of mitochondrial DNA (mtDNA) and its levels in the cell, which are the key elements to consider when trying to achieve molecular identification in ancient and degraded samples. mtDNA sequence analysis has been appropriately validated and is a consistent molecular target for the examination of biological evidence encountered in forensic cases—and profiling, in certain conditions—especially for burnt bodies and degraded samples of all types. Exceptional cases and samples will be discussed in this review, such as mtDNA from leather in Beethoven’s grand piano, mtDNA in mummies, and solving famous historical criminal cases. In addition, this review will be discussing the use of ancient mtDNA to understand past human diet, to trace historical civilizations and ancient trade routes, and to uncover geographical domestication origins and lineage relationships. In each topic, we will present the power of mtDNA and how, in many cases, no nuclear DNA was left, leaving mitochondrial DNA analysis as a powerful alternative. Exploring this powerful tool further will be extremely useful to modern science and researchers, due to its capabilities in providing us with previously unattainable knowledge.
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Pereira JB, Costa MD, Vieira D, Pala M, Bamford L, Harich N, Cherni L, Alshamali F, Hatina J, Rychkov S, Stefanescu G, King T, Torroni A, Soares P, Pereira L, Richards MB. Reconciling evidence from ancient and contemporary genomes: a major source for the European Neolithic within Mediterranean Europe. Proc Biol Sci 2018; 284:rspb.2016.1976. [PMID: 28330913 DOI: 10.1098/rspb.2016.1976] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 02/14/2017] [Indexed: 11/12/2022] Open
Abstract
Important gaps remain in our understanding of the spread of farming into Europe, due partly to apparent contradictions between studies of contemporary genetic variation and ancient DNA. It seems clear that farming was introduced into central, northern, and eastern Europe from the south by pioneer colonization. It is often argued that these dispersals originated in the Near East, where the potential source genetic pool resembles that of the early European farmers, but clear ancient DNA evidence from Mediterranean Europe is lacking, and there are suggestions that Mediterranean Europe may have resembled the Near East more than the rest of Europe in the Mesolithic. Here, we test this proposal by dating mitogenome founder lineages from the Near East in different regions of Europe. We find that whereas the lineages date mainly to the Neolithic in central Europe and Iberia, they largely date to the Late Glacial period in central/eastern Mediterranean Europe. This supports a scenario in which the genetic pool of Mediterranean Europe was partly a result of Late Glacial expansions from a Near Eastern refuge, and that this formed an important source pool for subsequent Neolithic expansions into the rest of Europe.
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Affiliation(s)
- Joana B Pereira
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,Instituto de Investigacão e Inovacão em Saúde (i3S), Universidade do Porto, Porto 4200-135, Portugal.,Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto 4200-465, Portugal
| | - Marta D Costa
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto 4200-465, Portugal.,Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.,ICVS/3Bs-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Daniel Vieira
- Department of Biology, CBMA (Centre of Molecular and Environmental Biology), University of Minho, Braga, Portugal
| | - Maria Pala
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK
| | - Lisa Bamford
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Nourdin Harich
- Laboratoire d'Anthropogenetique, Department de Biologie, Universite Chouaib Doukkali, El Jadida 24000, Morocco
| | - Lotfi Cherni
- Laboratory of Genetics, Immunology and Human Pathology, Faculté de Sciences de Tunis, Université de Tunis El Manar, Tunis 2092, Tunisia.,Tunis and High Institute of Biotechnology, University of Monastir, 5000 Monastir, Tunisia
| | - Farida Alshamali
- General Department of Forensic Sciences and Criminology, Dubai Police General Headquarters, Dubai 1493, United Arab Emirates
| | - Jiři Hatina
- Medical Faculty in Pilsen, Institute of Biology, Charles University, Pilsen, Czech Republic
| | | | | | - Turi King
- Department of Genetics, University of Leicester, Adrian Building, University Road, Leicester LE1 7RH, UK
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie 'L. Spallanzani', Università di Pavia, Pavia, Italy
| | - Pedro Soares
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto 4200-465, Portugal.,Department of Biology, CBMA (Centre of Molecular and Environmental Biology), University of Minho, Braga, Portugal
| | - Luísa Pereira
- Instituto de Investigacão e Inovacão em Saúde (i3S), Universidade do Porto, Porto 4200-135, Portugal.,Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto 4200-465, Portugal.,Faculdade de Medicina da Universidade do Porto, Porto 4200-319, Portugal
| | - Martin B Richards
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK .,Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK
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6
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Ancient mitogenomes of Phoenicians from Sardinia and Lebanon: A story of settlement, integration, and female mobility. PLoS One 2018; 13:e0190169. [PMID: 29320542 PMCID: PMC5761892 DOI: 10.1371/journal.pone.0190169] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 12/08/2017] [Indexed: 11/19/2022] Open
Abstract
The Phoenicians emerged in the Northern Levant around 1800 BCE and by the 9th century BCE had spread their culture across the Mediterranean Basin, establishing trading posts, and settlements in various European Mediterranean and North African locations. Despite their widespread influence, what is known of the Phoenicians comes from what was written about them by the Greeks and Egyptians. In this study, we investigate the extent of Phoenician integration with the Sardinian communities they settled. We present 14 new ancient mitogenome sequences from pre-Phoenician (~1800 BCE) and Phoenician (~700–400 BCE) samples from Lebanon (n = 4) and Sardinia (n = 10) and compare these with 87 new complete mitogenomes from modern Lebanese and 21 recently published pre-Phoenician ancient mitogenomes from Sardinia to investigate the population dynamics of the Phoenician (Punic) site of Monte Sirai, in southern Sardinia. Our results indicate evidence of continuity of some lineages from pre-Phoenician populations suggesting integration of indigenous Sardinians in the Monte Sirai Phoenician community. We also find evidence of the arrival of new, unique mitochondrial lineages, indicating the movement of women from sites in the Near East or North Africa to Sardinia, but also possibly from non-Mediterranean populations and the likely movement of women from Europe to Phoenician sites in Lebanon. Combined, this evidence suggests female mobility and genetic diversity in Phoenician communities, reflecting the inclusive and multicultural nature of Phoenician society.
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7
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Pimenta J, Lopes AM, Comas D, Amorim A, Arenas M. Evaluating the Neolithic Expansion at Both Shores of the Mediterranean Sea. Mol Biol Evol 2017; 34:3232-3242. [DOI: 10.1093/molbev/msx256] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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The ancient cline of haplogroup K implies that the Neolithic transition in Europe was mainly demic. Sci Rep 2017; 7:11229. [PMID: 28894281 PMCID: PMC5594011 DOI: 10.1038/s41598-017-11629-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 08/29/2017] [Indexed: 11/09/2022] Open
Abstract
Using a database with the mitochondrial DNA (mtDNA) of 513 Neolithic individuals, we quantify the space-time variation of the frequency of haplogroup K, previously proposed as a relevant Neolithic marker. We compare these data to simulations, based on a mathematical model in which a Neolithic population spreads from Syria to Anatolia and Europe, possibly interbreeding with Mesolithic individuals (who lack haplogroup K) and/or teaching farming to them. Both the data and the simulations show that the percentage of haplogroup K (%K) decreases with increasing distance from Syria and that, in each region, the %K tends to decrease with increasing time after the arrival of farming. Both the model and the data display a local minimum of the genetic cline, and for the same Neolithic regional culture (Sweden). Comparing the observed ancient cline of haplogroup K to the simulation results reveals that about 98% of farmers were not involved in interbreeding neither acculturation (cultural diffusion). Therefore, cultural diffusion involved only a tiny fraction (about 2%) of farmers and, in this sense, the most relevant process in the spread of the Neolithic in Europe was demic diffusion (i.e., the dispersal of farmers), as opposed to cultural diffusion (i.e., the incorporation of hunter-gatherers).
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9
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López-Onaindia D, Subirà ME. Prehistoric funerary complexity in northern Iberia studied by using dental morphology. HOMO-JOURNAL OF COMPARATIVE HUMAN BIOLOGY 2017; 68:122-133. [PMID: 28365126 DOI: 10.1016/j.jchb.2017.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 12/07/2016] [Indexed: 11/19/2022]
Abstract
During the Neolithic Age and afterwards, several funerary practices coexisted in the northeast of the Iberian Peninsula from the Mediterranean to the Atlantic. According to archaeological data, there was a coexistence of sepulchral caves and megalithic monuments at the end of the Neolithic, following the dominance of open-air pit burials during the Middle Neolithic. The aim of this work is to analyze the biological relationships between individuals representing those cultures, based on their dental morphology - the first such attempt. This study presents data of 156 individuals from this period, and will allow elucidate the population dynamics including the role of migrations and other factors. The results indicate that there were no significant differences between the groups living in Atlantic and Mediterranean areas. Moreover, pairwise comparisons for each trait only show two significant results. This lack of differences could be related to trade activities between the two basins, which would contribute to individual exchanges between groups. Furthermore, according to biological affinities, trade activities along the Mediterranean Sea had a more marked influence over the Catalan populations than those from the Atlantic basin. There are no biological differences between groups representing the open-air pit culture and the sepulchral caves in each area. Finally, the megalithic groups from the Atlantic basin differ the most from the surrounding populations. This could be indicative of a slightly different biological origin of the people related to this culture.
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Affiliation(s)
- Diego López-Onaindia
- GRAPAC (Grup de Recerca Aplicada al Patrimoni Cultural), Unitat d'Antropologia Biològica, Departament BABVE, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.
| | - M Eulàlia Subirà
- GRAPAC (Grup de Recerca Aplicada al Patrimoni Cultural), Unitat d'Antropologia Biològica, Departament BABVE, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.
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10
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Carreras-Torres R, Ferran A, Zanetti D, Esteban E, Varesi L, Pojskic N, Coia V, Chaabani H, Via M, Moral P. Population structure from NOS genes correlates with geographical differences in coronary incidence across Europe. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2016; 161:634-645. [PMID: 27500977 DOI: 10.1002/ajpa.23063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 06/19/2016] [Accepted: 07/26/2016] [Indexed: 11/05/2022]
Abstract
OBJECTIVES The population analysis of cardiovascular risk and non-risk genetic variation can help to identify adaptive or random demographic processes that shaped coronary incidence variation across geography. MATERIAL AND METHODS In this study, 114 single nucleotide polymorphisms and 17 tandem repeat polymorphisms from Nitric Oxide Synthases (NOS) regions were analyzed in 1686 individuals from 35 populations from Europe, North Africa, and the Middle East. NOS genes encode for key enzymes on nitric oxide availability, which is involved in several cardiovascular processes. These genetic variations were used to test for selection and to infer the population structure of NOS regions. Moreover, we tested whether the variation in the incidence of coronary events and in the levels of classical risk factors in 11 of these European populations could be explained by the population structure estimates. RESULTS Our results supported, first, the absence of clear signs of selection for NOS genetic variants associated with cardiovascular diseases, and second, the presence of a continuous genetic pattern of variation across European and North African populations without a Mediterranean barrier for gene flow. Finally, population structure estimates from NOS regions are closely correlated with coronary event rates and classical risk parameters (explaining 39-98%) among European populations. CONCLUSION Our results reinforce the hypothesis that genetic bases of cardiovascular diseases and associated complex phenotypes could be geographically shaped by random demographic processes.
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Affiliation(s)
- Robert Carreras-Torres
- Departament Biologia Animal, Unitat d'Antropologia, Facultat de Biologia, Universitat de Barcelona, Spain
| | - Albert Ferran
- Departament Biologia Animal, Unitat d'Antropologia, Facultat de Biologia, Universitat de Barcelona, Spain
| | - Daniela Zanetti
- Departament Biologia Animal, Unitat d'Antropologia, Facultat de Biologia, Universitat de Barcelona, Spain
| | - Esther Esteban
- Departament Biologia Animal, Unitat d'Antropologia, Facultat de Biologia, Universitat de Barcelona, Spain.,Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Spain
| | - Laurent Varesi
- Laboratoire de virologie, Faculté des Sciences et Techniques, Université de Corse, France
| | - Naris Pojskic
- Laboratory for Molecular Genetics of Natural Resources, Institute for Genetic Engineering and Biotechnology, University of Sarajevo, Bosnia and Herzegovina
| | - Valentina Coia
- Accademia Europea di Bolzano (EURAC), Istituto per le Mummie e l'Iceman, Bolzano, Italy
| | - Hassen Chaabani
- Laboratory of Human Genetics and Anthropology, Faculty of Pharmacy, University of Monastir, Tunisia
| | - Marc Via
- Departament Psicologia Clínica i Psicobiologia and Institute of Neurosciences (UBNEURO), Universitat de Barcelona, Spain.,Institut de Recerca Pediàtrica Hospital Sant Joan de Déu (IRP_HSJD), Barcelona, Spain
| | - Pedro Moral
- Departament Biologia Animal, Unitat d'Antropologia, Facultat de Biologia, Universitat de Barcelona, Spain.,Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Spain
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Simón M, Díaz N, Solórzano E, Montiel R, Francalacci P, Malgosa A. Dissecting mitochondrial dna variability of balearic populations from the bronze age to the current era. Am J Hum Biol 2016; 29. [PMID: 27292871 DOI: 10.1002/ajhb.22883] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 05/15/2016] [Accepted: 05/17/2016] [Indexed: 11/06/2022] Open
Abstract
OBJECTIVES To determine ancient population influences on ancient and current Balearic populations and to reconstruct their mitochondrial DNA (mtDNA) gene pool evolution. METHODS We analyzed 239 individuals belonging to five archaeological populations from Majorca and Minorca, four dating to the transition between the Bronze Age and the Iron Age, and one Late Roman Majorcan population. Six additional individuals from Santa Teresa di Gallura from the Nuragic period were characterized and added to the existing samples from that culture to make comparisons with Talaiotic populations. RESULTS We characterized the haplogroups of 138 individuals and obtained 69 sequences from mtDNA hypervariable region I. In the intra-island study, the apparent differences in social and funerary rites between two contiguous Majorcan necropolises were correlated with genetic characteristics. Also, the likely occurrence of consanguinity in a population with a very particular burial pattern was supported by genetic data. Despite the uniqueness of each necropolis, the global comparison of the five necropolises revealed no significant differences between them, or between ancient and modern populations from the islands. Ancient Balearics showed a similar mtDNA gene pool to Ancient Catalans, had a Near Eastern component, and showed continuity with European populations since at least the Bronze Age. CONCLUSION We characterized five Balearic necropolises in the context of their geographic and cultural characteristics. The similarity between ancient Balearic and ancient Catalan gene pools reinforces their known historic interactions, while the lack of a consistent genetic continuity with Ancient Sardinians suggests that Talaiotic and Nuragic cultures arose in differentiated populations. Am. J. Hum. Biol. 29:e22883, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Marc Simón
- Unitat d'Antropologia Biològica, Departament BABVE, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - Nancy Díaz
- Universidad de los Andes. Avenida 3, Independencia. Edificio el Rectorado, Mérida, 5101, Venezuela
| | - Eduvigis Solórzano
- Universidad de los Andes. Avenida 3, Independencia. Edificio el Rectorado, Mérida, 5101, Venezuela
| | - Rafael Montiel
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada, CINVESTAV-IPN. Km. 9.6 Libramiento Norte Carretera Irapuato, Irapuato, 36821, Mexico
| | - Paolo Francalacci
- Universitá di Sassari, Piazza D'Armi, 17, Sassari, SS, 07100, Italia
| | - Assumpció Malgosa
- Unitat d'Antropologia Biològica, Departament BABVE, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
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12
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Núñez C, Baeta M, Cardoso S, Palencia-Madrid L, García-Romero N, Llanos A, M. de Pancorbo M. Mitochondrial DNA Reveals the Trace of the Ancient Settlers of a Violently Devastated Late Bronze and Iron Ages Village. PLoS One 2016; 11:e0155342. [PMID: 27176817 PMCID: PMC4866787 DOI: 10.1371/journal.pone.0155342] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 04/27/2016] [Indexed: 11/19/2022] Open
Abstract
La Hoya (Alava, Basque Country) was one of the most important villages of the Late Bronze and Iron Ages of the north of the Iberian Peninsula, until it was violently devastated around the 4th century and abandoned in the 3rd century B.C. Archaeological evidences suggest that descendants from La Hoya placed their new settlement in a nearby hill, which gave rise to the current village of Laguardia. In this study, we have traced the genetic imprints of the extinct inhabitants of La Hoya through the analysis of maternal lineages. In particular, we have analyzed the mitochondrial DNA (mtDNA) control region of 41 human remains recovered from the archaeological site for comparison with a sample of 51 individuals from the geographically close present-day population of Laguardia, as well as 56 individuals of the general population of the province of Alava, where the archaeological site and Laguardia village are located. MtDNA haplotypes were successfully obtained in 25 out of 41 ancient samples, and 14 different haplotypes were identified. The major mtDNA subhaplogroups observed in La Hoya were H1, H3, J1 and U5, which show a distinctive frequency pattern in the autochthonous populations of the north of the Iberian Peninsula. Approximate Bayesian Computation analysis was performed to test the most likely model for the local demographic history. The results did not sustain a genealogical continuity between Laguardia and La Hoya at the haplotype level, although factors such as sampling effects, recent admixture events, and genetic bottlenecks need to be considered. Likewise, the highly similar subhaplogroup composition detected between La Hoya and Laguardia and Alava populations do not allow us to reject a maternal genetic continuity in the human groups of the area since at least the Iron Age to present times. Broader analyses, based on a larger collection of samples and genetic markers, would be required to study fine-scale population events in these human groups.
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Affiliation(s)
- Carolina Núñez
- BIOMICs Research Group, Centro de Investigación “Lascaray” Ikergunea, Universidad del País Vasco (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Miriam Baeta
- BIOMICs Research Group, Centro de Investigación “Lascaray” Ikergunea, Universidad del País Vasco (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Sergio Cardoso
- BIOMICs Research Group, Centro de Investigación “Lascaray” Ikergunea, Universidad del País Vasco (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Leire Palencia-Madrid
- BIOMICs Research Group, Centro de Investigación “Lascaray” Ikergunea, Universidad del País Vasco (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Noemí García-Romero
- BIOMICs Research Group, Centro de Investigación “Lascaray” Ikergunea, Universidad del País Vasco (UPV/EHU), Vitoria-Gasteiz, Spain
| | | | - Marian M. de Pancorbo
- BIOMICs Research Group, Centro de Investigación “Lascaray” Ikergunea, Universidad del País Vasco (UPV/EHU), Vitoria-Gasteiz, Spain
- * E-mail:
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13
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Fort J. Demic and cultural diffusion propagated the Neolithic transition across different regions of Europe. J R Soc Interface 2016; 12. [PMID: 25977959 PMCID: PMC4424695 DOI: 10.1098/rsif.2015.0166] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The Neolithic transition is the shift from hunting–gathering into farming. About 9000 years ago, the Neolithic transition began to spread from the Near East into Europe, until it reached Northern Europe about 5500 years ago. There are two main models of this spread. The demic model assumes that it was mainly due to the reproduction and dispersal of farmers. The cultural model assumes that European hunter–gatherers become farmers by acquiring domestic plants and animals, as well as knowledge, from neighbouring farmers. Here we use the dates of about 900 archaeological sites to compute a speed map of the spread of the Neolithic transition in Europe. We compare the speed map to the speed ranges predicted by purely demic, demic–cultural and purely cultural models. The comparison indicates that the transition was cultural in Northern Europe, the Alpine region and west of the Black Sea. But demic diffusion was at work in other regions such as the Balkans and Central Europe. Our models can be applied to many other cultural traits. We also propose that genetic data could be gathered and used to measure the demic kernels of Early Neolithic populations. This would lead to an enormous advance in Neolithic spread modelling.
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14
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Alt KW, Zesch S, Garrido-Pena R, Knipper C, Szécsényi-Nagy A, Roth C, Tejedor-Rodríguez C, Held P, García-Martínez-de-Lagrán Í, Navitainuck D, Arcusa Magallón H, Rojo-Guerra MA. A Community in Life and Death: The Late Neolithic Megalithic Tomb at Alto de Reinoso (Burgos, Spain). PLoS One 2016; 11:e0146176. [PMID: 26789731 PMCID: PMC4720281 DOI: 10.1371/journal.pone.0146176] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 12/13/2015] [Indexed: 11/19/2022] Open
Abstract
The analysis of the human remains from the megalithic tomb at Alto de Reinoso represents the widest integrative study of a Neolithic collective burial in Spain. Combining archaeology, osteology, molecular genetics and stable isotope analysis (87Sr/86Sr, δ15N, δ13C) it provides a wealth of information on the minimum number of individuals, age, sex, body height, pathologies, mitochondrial DNA profiles, kinship relations, mobility, and diet. The grave was in use for approximately one hundred years around 3700 cal BC, thus dating from the Late Neolithic of the Iberian chronology. At the bottom of the collective tomb, six complete and six partial skeletons lay in anatomically correct positions. Above them, further bodies represented a subsequent and different use of the tomb, with almost all of the skeletons exhibiting signs of manipulation such as missing skeletal parts, especially skulls. The megalithic monument comprised at least 47 individuals, including males, females, and subadults, although children aged 0-6 years were underrepresented. The skeletal remains exhibited a moderate number of pathologies, such as degenerative joint diseases, healed fractures, cranial trauma, and a low intensity of caries. The mitochondrial DNA profiles revealed a pattern pointing to a closely related local community with matrilineal kinship patterns. In some cases adjacent individuals in the bottom layer showed familial relationships. According to their strontium isotope ratios, only a few individuals were likely to have spent their early childhood in a different geological environment, whilst the majority of individuals grew up locally. Carbon and nitrogen isotope analysis, which was undertaken to reconstruct the dietary habits, indicated that this was a homogeneous group with egalitarian access to food. Cereals and small ruminants were the principal sources of nutrition. These data fit in well with a lifestyle typical of sedentary farming populations in the Spanish Meseta during this period of the Neolithic.
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Affiliation(s)
- Kurt W. Alt
- Danube Private University, Krems, Austria
- Institute for Prehistory and Archaeological Science and Hightech Research Center, Basel University, Basel, Switzerland
- State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, Halle, Germany
- * E-mail:
| | - Stephanie Zesch
- German Mummy Project, Reiss-Engelhorn-Museen, Mannheim, Germany
| | - Rafael Garrido-Pena
- Department of Prehistory and Archaeology, Faculty of Philosophy and Letters, Autonomous University of Madrid, Madrid, Spain
| | - Corina Knipper
- Curt Engelhorn Centre Archaeometry gGmbH, Mannheim, Germany
| | - Anna Szécsényi-Nagy
- Laboratory of Archaeogenetics, Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest, Hungary
| | - Christina Roth
- Institute of Anthropology, Mainz University, Mainz, Germany
| | | | - Petra Held
- Department of Applied and Analytical Paleontology, Mainz University, Mainz, Germany
| | - Íñigo García-Martínez-de-Lagrán
- Department of Prehistory, University of the Basque Government, Vitoria, Spain
- Laboratoire TRACES UMR5608, Université de Toulouse, Toulouse, France
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Malmström H, Linderholm A, Skoglund P, Storå J, Sjödin P, Gilbert MTP, Holmlund G, Willerslev E, Jakobsson M, Lidén K, Götherström A. Ancient mitochondrial DNA from the northern fringe of the Neolithic farming expansion in Europe sheds light on the dispersion process. Philos Trans R Soc Lond B Biol Sci 2015; 370:20130373. [PMID: 25487325 DOI: 10.1098/rstb.2013.0373] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The European Neolithization process started around 12 000 years ago in the Near East. The introduction of agriculture spread north and west throughout Europe and a key question has been if this was brought about by migrating individuals, by an exchange of ideas or a by a mixture of these. The earliest farming evidence in Scandinavia is found within the Funnel Beaker Culture complex (Trichterbecherkultur, TRB) which represents the northernmost extension of Neolithic farmers in Europe. The TRB coexisted for almost a millennium with hunter-gatherers of the Pitted Ware Cultural complex (PWC). If migration was a substantial part of the Neolithization, even the northerly TRB community would display a closer genetic affinity to other farmer populations than to hunter-gatherer populations. We deep-sequenced the mitochondrial hypervariable region 1 from seven farmers (six TRB and one Battle Axe complex, BAC) and 13 hunter-gatherers (PWC) and authenticated the sequences using postmortem DNA damage patterns. A comparison with 124 previously published sequences from prehistoric Europe shows that the TRB individuals share a close affinity to Central European farmer populations, and that they are distinct from hunter-gatherer groups, including the geographically close and partially contemporary PWC that show a close affinity to the European Mesolithic hunter-gatherers.
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Affiliation(s)
- Helena Malmström
- Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
| | - Anna Linderholm
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, 106 91 Stockholm, Sweden Durham Evolution and Ancient DNA, Department of Archaeology, Durham University, South Road, Durham DH1 3LE, UK
| | - Pontus Skoglund
- Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
| | - Jan Storå
- Osteolarchaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, 106 91 Stockholm, Sweden
| | - Per Sjödin
- Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Volgade 5-7, 1350 Copenhagen, Denmark
| | - Gunilla Holmlund
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping University, Artillerigatan 12, 587 58, Linköping, Sweden Department of Clinical and Experimental Medicine, Linköping University, Artillerigatan 12, 587 58, Linköping, Sweden
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Volgade 5-7, 1350 Copenhagen, Denmark
| | - Mattias Jakobsson
- Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Kerstin Lidén
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, 106 91 Stockholm, Sweden
| | - Anders Götherström
- Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, 106 91 Stockholm, Sweden
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16
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Vestiges of an Ancient Border in the Contemporary Genetic Diversity of North-Eastern Europe. PLoS One 2015; 10:e0130331. [PMID: 26132657 PMCID: PMC4488853 DOI: 10.1371/journal.pone.0130331] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Accepted: 05/19/2015] [Indexed: 11/25/2022] Open
Abstract
It has previously been demonstrated that the advance of the Neolithic Revolution from the Near East through Europe was decelerated in the northernmost confines of the continent, possibly as a result of space and resource competition with lingering Mesolithic populations. Finland was among the last domains to adopt a farming lifestyle, and is characterized by substructuring in the form of a distinct genetic border dividing the northeastern and southwestern regions of the country. To explore the origins of this divergence, the geographical patterns of mitochondrial and Y-chromosomal haplogroups of Neolithic and Mesolithic ancestry were assessed in Finnish populations. The distribution of these uniparental markers revealed a northeastern bias for hunter-gatherer haplogroups, while haplogroups associated with the farming lifestyle clustered in the southwest. In addition, a correlation could be observed between more ancient mitochondrial haplogroup age and eastern concentration. These results coupled with prior archeological evidence suggest the genetic northeast/southwest division observed in contemporary Finland represents an ancient vestigial border between Mesolithic and Neolithic populations undetectable in most other regions of Europe.
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17
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Zupan A, Hauptman N, Glavač D. The maternal perspective for five Slovenian regions: The importance of regional sampling. Ann Hum Biol 2015; 43:57-66. [PMID: 26065896 DOI: 10.3109/03014460.2015.1006678] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND The Slovenian territory is geographically positioned between the Alps, Adriatic Sea, Pannonian basin and the Dinaric Mountains and, as such, has served as a passageway for various populations in different periods of time. Turbulent historic events and diverse geography of the region have produced a diverse contemporary population whose genetic analysis could provide insight into past demographic events. AIM The aims of this study were to characterize the Slovenian mitochondrial gene pool at the micro-geographic level and to compare it with surrounding populations. SUBJECTS AND METHODS A total of 402 individuals from five Slovenian regions were analysed in this study by typing HVR I, HVR II and coding region polymorphisms of mtDNA. RESULTS Analysis revealed 47 haplogroups and sub-haplogroups, the most common of which were H*, H1, J1c, T2 and U5a. Intra-population comparisons revealed a sharp gradient of the J1c haplogroup between Slovenian regions, with a peak frequency of 24.5% being observed in the population of the Littoral Region. CONCLUSION The sharp gradient of the J1c haplogroup between Slovenian regions is in line with the archaeological horizon known as Impressed Ware culture and could, therefore, represent a genetic trace of the early Neolithic expansion route along the East Adriatic coastal region.
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Affiliation(s)
- Andrej Zupan
- a Department of Molecular Genetics , Institute of Pathology, Faculty of Medicine, University of Ljubljana , Ljubljana , Slovenia
| | - Nina Hauptman
- a Department of Molecular Genetics , Institute of Pathology, Faculty of Medicine, University of Ljubljana , Ljubljana , Slovenia
| | - Damjan Glavač
- a Department of Molecular Genetics , Institute of Pathology, Faculty of Medicine, University of Ljubljana , Ljubljana , Slovenia
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18
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Hervella M, Rotea M, Izagirre N, Constantinescu M, Alonso S, Ioana M, Lazăr C, Ridiche F, Soficaru AD, Netea MG, de-la-Rua C. Ancient DNA from South-East Europe Reveals Different Events during Early and Middle Neolithic Influencing the European Genetic Heritage. PLoS One 2015; 10:e0128810. [PMID: 26053041 PMCID: PMC4460020 DOI: 10.1371/journal.pone.0128810] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 04/30/2015] [Indexed: 01/26/2023] Open
Abstract
The importance of the process of Neolithization for the genetic make-up of European populations has been hotly debated, with shifting hypotheses from a demic diffusion (DD) to a cultural diffusion (CD) model. In this regard, ancient DNA data from the Balkan Peninsula, which is an important source of information to assess the process of Neolithization in Europe, is however missing. In the present study we show genetic information on ancient populations of the South-East of Europe. We assessed mtDNA from ten sites from the current territory of Romania, spanning a time-period from the Early Neolithic to the Late Bronze Age. mtDNA data from Early Neolithic farmers of the Starčevo Criş culture in Romania (Cârcea, Gura Baciului and Negrileşti sites), confirm their genetic relationship with those of the LBK culture (Linienbandkeramik Kultur) in Central Europe, and they show little genetic continuity with modern European populations. On the other hand, populations of the Middle-Late Neolithic (Boian, Zau and Gumelniţa cultures), supposedly a second wave of Neolithic migration from Anatolia, had a much stronger effect on the genetic heritage of the European populations. In contrast, we find a smaller contribution of Late Bronze Age migrations to the genetic composition of Europeans. Based on these findings, we propose that permeation of mtDNA lineages from a second wave of Middle-Late Neolithic migration from North-West Anatolia into the Balkan Peninsula and Central Europe represent an important contribution to the genetic shift between Early and Late Neolithic populations in Europe, and consequently to the genetic make-up of modern European populations.
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Affiliation(s)
- Montserrat Hervella
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Bizkaia, Spain
| | - Mihai Rotea
- National History Museum of Transylvania, Cluj-Napoca, Romania
| | - Neskuts Izagirre
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Bizkaia, Spain
| | - Mihai Constantinescu
- “Francisc I. Rainer" Institute of Anthropology, Romanian Academy, Bucharest, Romania
| | - Santos Alonso
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Bizkaia, Spain
| | - Mihai Ioana
- Department of Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Cătălin Lazăr
- National History Museum of Romania, Bucharest, Romania
| | | | | | - Mihai G. Netea
- Department of Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
- Radboud Center for Infectious Diseases, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
- * E-mail: (CR); (MN)
| | - Concepcion de-la-Rua
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Bizkaia, Spain
- * E-mail: (CR); (MN)
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19
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Rivollat M, Mendisco F, Pemonge MH, Safi A, Saint-Marc D, Brémond A, Couture-Veschambre C, Rottier S, Deguilloux MF. When the waves of European Neolithization met: first paleogenetic evidence from early farmers in the southern Paris Basin. PLoS One 2015; 10:e0125521. [PMID: 25928633 PMCID: PMC4415815 DOI: 10.1371/journal.pone.0125521] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 03/14/2015] [Indexed: 11/19/2022] Open
Abstract
An intense debate concerning the nature and mode of Neolithic transition in Europe has long received much attention. Recent publications of paleogenetic analyses focusing on ancient European farmers from Central Europe or the Iberian Peninsula have greatly contributed to this debate, providing arguments in favor of major migrations accompanying European Neolithization and highlighting noticeable genetic differentiation between farmers associated with two archaeologically defined migration routes: the Danube valley and the Mediterranean Sea. The aim of the present study was to fill a gap with the first paleogenetic data of Neolithic settlers from a region (France) where the two great currents came into both direct and indirect contact with each other. To this end, we analyzed the Gurgy 'Les Noisats' group, an Early/Middle Neolithic necropolis in the southern part of the Paris Basin. Interestingly, the archaeological record from this region highlighted a clear cultural influence from the Danubian cultural sphere but also notes exchanges with the Mediterranean cultural area. To unravel the processes implied in these cultural exchanges, we analyzed 102 individuals and obtained the largest Neolithic mitochondrial gene pool so far (39 HVS-I mitochondrial sequences and haplogroups for 55 individuals) from a single archaeological site from the Early/Middle Neolithic period. Pairwise FST values, haplogroup frequencies and shared informative haplotypes were calculated and compared with ancient and modern European and Near Eastern populations. These descriptive analyses provided patterns resulting from different evolutionary scenarios; however, the archaeological data available for the region suggest that the Gurgy group was formed through equivalent genetic contributions of farmer descendants from the Danubian and Mediterranean Neolithization waves. However, these results, that would constitute the most ancient genetic evidence of admixture between farmers from both Central and Mediterranean migration routes in the European Neolithization debate, are subject to confirmation through appropriate model-based approaches.
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Affiliation(s)
- Maïté Rivollat
- De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie—UMR 5199, University of Bordeaux, Bordeaux, France
| | - Fanny Mendisco
- De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie—UMR 5199, University of Bordeaux, Bordeaux, France
| | - Marie-Hélène Pemonge
- De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie—UMR 5199, University of Bordeaux, Bordeaux, France
| | - Audrey Safi
- De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie—UMR 5199, University of Bordeaux, Bordeaux, France
| | - Didier Saint-Marc
- De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie—UMR 5199, University of Bordeaux, Bordeaux, France
| | - Antoine Brémond
- De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie—UMR 5199, University of Bordeaux, Bordeaux, France
| | - Christine Couture-Veschambre
- De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie—UMR 5199, University of Bordeaux, Bordeaux, France
| | - Stéphane Rottier
- De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie—UMR 5199, University of Bordeaux, Bordeaux, France
| | - Marie-France Deguilloux
- De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie—UMR 5199, University of Bordeaux, Bordeaux, France
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20
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Keller M, Rott A, Hoke N, Schwarzberg H, Regner-Kamlah B, Harbeck M, Wahl J. United in death-related by blood? Genetic and archeometric analyses of skeletal remains from the neolithic earthwork bruchsal-aue. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2015; 157:458-71. [DOI: 10.1002/ajpa.22738] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 02/16/2015] [Accepted: 02/22/2015] [Indexed: 11/12/2022]
Affiliation(s)
- Marcel Keller
- Anthropology and Environmental History; Department Biology I; Ludwig-Maximilians-University Munich; D-82152 Martinsried Germany
| | - Andreas Rott
- Department of Anthropology; State Collection for Anthropology and Palaeoanatomy; D-80333 Munich Germany
| | - Nadja Hoke
- Anthropology and Environmental History; Department Biology I; Ludwig-Maximilians-University Munich; D-82152 Martinsried Germany
- Department of Anthropology; State Collection for Anthropology and Palaeoanatomy; D-80333 Munich Germany
| | - Heiner Schwarzberg
- Department of Prehistory; Bavarian State Archaeological Collection; D-80538 Munich Germany
| | - Birgit Regner-Kamlah
- Department of Archaeological Heritage Management 84.2; State Office for Cultural Heritage Management Baden-Württemberg, State Regional Authority Stuttgart; D-76133 Karlsruhe Germany
| | - Michaela Harbeck
- Department of Anthropology; State Collection for Anthropology and Palaeoanatomy; D-80333 Munich Germany
| | - Joachim Wahl
- Department of Archaeological Heritage Management 84.1; State Office for Cultural Heritage Management Baden-Württemberg, State Regional Authority Stuttgart; D-78467 Constance Germany
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21
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Major transitions in human evolution revisited: a tribute to ancient DNA. J Hum Evol 2014; 79:4-20. [PMID: 25532800 DOI: 10.1016/j.jhevol.2014.06.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 06/06/2014] [Accepted: 06/19/2014] [Indexed: 11/23/2022]
Abstract
The origin and diversification of modern humans have been characterized by major evolutionary transitions and demographic changes. Patterns of genetic variation within modern populations can help with reconstructing this ∼200 thousand year-long population history. However, by combining this information with genomic data from ancient remains, one can now directly access our evolutionary past and reveal our population history in much greater detail. This review outlines the main recent achievements in ancient DNA research and illustrates how the field recently moved from the polymerase chain reaction (PCR) amplification of short mitochondrial fragments to whole-genome sequencing and thereby revisited our own history. Ancient DNA research has revealed the routes that our ancestors took when colonizing the planet, whom they admixed with, how they domesticated plant and animal species, how they genetically responded to changes in lifestyle, and also, which pathogens decimated their populations. These approaches promise to soon solve many pending controversies about our own origins that are indecipherable from modern patterns of genetic variation alone, and therefore provide an extremely powerful toolkit for a new generation of molecular anthropologists.
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22
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Aspects of ancient mitochondrial DNA analysis in different populations for understanding human evolution. Balkan J Med Genet 2014; 17:5-14. [PMID: 25741209 PMCID: PMC4347471 DOI: 10.2478/bjmg-2014-0019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The evolution of modern humans is a long and difficult process which started from their first appearance and continues to the present day. The study of the genetic origin of populations can help to determine population kinship and to better understand the gradual changes of the gene pool in space and time. Mitochondrial DNA (mtDNA) is a proper tool for the determination of the origin of populations due to its high evolutionary importance. Ancient mitochondrial DNA retrieved from museum specimens, archaeological finds and fossil remains can provide direct evidence for population origins and migration processes. Despite the problems with contaminations and authenticity of ancient mitochondrial DNA, there is a developed set of criteria and platforms for obtaining authentic ancient DNA. During the last two decades, the application of different methods and techniques for analysis of ancient mitochondrial DNA gave promising results. Still, the literature is relatively poor with information for the origin of human populations. Using comprehensive phylogeographic and population analyses we can observe the development and formation of the contemporary populations. The aim of this study was to shed light on human migratory processes and the formation of populations based on available ancient mtDNA data.
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Gómez-Sánchez D, Olalde I, Pierini F, Matas-Lalueza L, Gigli E, Lari M, Civit S, Lozano M, Vergès JM, Caramelli D, Ramírez O, Lalueza-Fox C. Mitochondrial DNA from El Mirador cave (Atapuerca, Spain) reveals the heterogeneity of Chalcolithic populations. PLoS One 2014; 9:e105105. [PMID: 25116044 PMCID: PMC4130614 DOI: 10.1371/journal.pone.0105105] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 07/18/2014] [Indexed: 12/31/2022] Open
Abstract
Previous mitochondrial DNA analyses on ancient European remains have suggested that the current distribution of haplogroup H was modeled by the expansion of the Bell Beaker culture (ca 4,500–4,050 years BP) out of Iberia during the Chalcolithic period. However, little is known on the genetic composition of contemporaneous Iberian populations that do not carry the archaeological tool kit defining this culture. Here we have retrieved mitochondrial DNA (mtDNA) sequences from 19 individuals from a Chalcolithic sample from El Mirador cave in Spain, dated to 4,760–4,200 years BP and we have analyzed the haplogroup composition in the context of modern and ancient populations. Regarding extant African, Asian and European populations, El Mirador shows affinities with Near Eastern groups. In different analyses with other ancient samples, El Mirador clusters with Middle and Late Neolithic populations from Germany, belonging to the Rössen, the Salzmünde and the Baalberge archaeological cultures but not with contemporaneous Bell Beakers. Our analyses support the existence of a common genetic signal between Western and Central Europe during the Middle and Late Neolithic and points to a heterogeneous genetic landscape among Chalcolithic groups.
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Affiliation(s)
- Daniel Gómez-Sánchez
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Iñigo Olalde
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Federica Pierini
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Laura Matas-Lalueza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Elena Gigli
- Laboratory of Anthropology, Department of Biology, University of Florence, Florence, Italy
| | - Martina Lari
- Laboratory of Anthropology, Department of Biology, University of Florence, Florence, Italy
| | - Sergi Civit
- Department of Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Marina Lozano
- Institut Català de Paleoecologia Humana i Evolució Social, Tarragona, Spain
| | - Josep Maria Vergès
- Institut Català de Paleoecologia Humana i Evolució Social, Tarragona, Spain
- Àrea de Prehistòria, Departament d’Història i Història de l’Art, Universitat Rovira i Virgili, Tarragona, Spain
| | - David Caramelli
- Laboratory of Anthropology, Department of Biology, University of Florence, Florence, Italy
| | - Oscar Ramírez
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- * E-mail:
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24
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Echoes from Sepharad: signatures on the maternal gene pool of crypto-Jewish descendants. Eur J Hum Genet 2014; 23:693-9. [PMID: 25074462 DOI: 10.1038/ejhg.2014.140] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 06/11/2014] [Accepted: 06/20/2014] [Indexed: 11/08/2022] Open
Abstract
The majority of genetic studies on Jewish populations have been focused on Ashkenazim, and genetic data from the Sephardic original source, the Iberian Peninsula, are particularly scarce. Regarding the mitochondrial genome, the available information is limited to a single Portuguese village, Belmonte, where just two different lineages (a single one corresponding to 93.3%) were found in 30 individuals. Aiming at disclosing the ancestral maternal background of the Portuguese Jewry, we enlarged the sampling to other crypto-Jewish descendants in the Bragança district (NE Portugal). Fifty-seven complete mtDNA genomes were newly sequenced and - in contrast with Belmonte - a high level of diversity was found, with five haplogroups (HV0b, N1, T2b11, T2e and U2e) being putatively identified as Sephardic founding lineages. Therefore - in sharp contrast with Belmonte - these communities have managed to escape the expected inbreeding effects caused by centuries of religious repression and have kept a significant proportion of the Sephardic founder gene pool. This deeper analysis of the surviving Sephardic maternal lineages allowed a much more comprehensive and detailed perspective on the origins and survival of the Sephardic genetic heritage. In line with previously published results on Sephardic paternal lineages, our findings also show a surprising resistance to the erosion of genetic diversity in the maternal lineages.
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Veeramah KR, Novembre J. Demographic events and evolutionary forces shaping European genetic diversity. Cold Spring Harb Perspect Biol 2014; 6:a008516. [PMID: 25059709 PMCID: PMC4142961 DOI: 10.1101/cshperspect.a008516] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Europeans have been the focus of some of the largest studies of genetic diversity in any species to date. Recent genome-wide data have reinforced the hypothesis that present-day European genetic diversity is strongly correlated with geography. The remaining challenge now is to understand more precisely how patterns of diversity in Europe reflect ancient demographic events such as postglacial expansions or the spread of farming. It is likely that recent advances in paleogenetics will give us some of these answers. There has also been progress in identifying specific segments of European genomes that reflect adaptations to selective pressures from the physical environment, disease, and dietary shifts. A growing understanding of how modern European genetic diversity has been shaped by demographic and evolutionary forces is not only of basic historical and anthropological interest but also aids genetic studies of disease.
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Affiliation(s)
- Krishna R Veeramah
- Arizona Research Laboratories Division of Biotechnology, University of Arizona, Tucson, Arizona 85721
| | - John Novembre
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637
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26
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Fernández E, Pérez-Pérez A, Gamba C, Prats E, Cuesta P, Anfruns J, Molist M, Arroyo-Pardo E, Turbón D. Ancient DNA analysis of 8000 B.C. near eastern farmers supports an early neolithic pioneer maritime colonization of Mainland Europe through Cyprus and the Aegean Islands. PLoS Genet 2014; 10:e1004401. [PMID: 24901650 PMCID: PMC4046922 DOI: 10.1371/journal.pgen.1004401] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 04/09/2014] [Indexed: 11/18/2022] Open
Abstract
The genetic impact associated to the Neolithic spread in Europe has been widely debated over the last 20 years. Within this context, ancient DNA studies have provided a more reliable picture by directly analyzing the protagonist populations at different regions in Europe. However, the lack of available data from the original Near Eastern farmers has limited the achieved conclusions, preventing the formulation of continental models of Neolithic expansion. Here we address this issue by presenting mitochondrial DNA data of the original Near-Eastern Neolithic communities with the aim of providing the adequate background for the interpretation of Neolithic genetic data from European samples. Sixty-three skeletons from the Pre Pottery Neolithic B (PPNB) sites of Tell Halula, Tell Ramad and Dja'de El Mughara dating between 8,700-6,600 cal. B.C. were analyzed, and 15 validated mitochondrial DNA profiles were recovered. In order to estimate the demographic contribution of the first farmers to both Central European and Western Mediterranean Neolithic cultures, haplotype and haplogroup diversities in the PPNB sample were compared using phylogeographic and population genetic analyses to available ancient DNA data from human remains belonging to the Linearbandkeramik-Alföldi Vonaldiszes Kerámia and Cardial/Epicardial cultures. We also searched for possible signatures of the original Neolithic expansion over the modern Near Eastern and South European genetic pools, and tried to infer possible routes of expansion by comparing the obtained results to a database of 60 modern populations from both regions. Comparisons performed among the 3 ancient datasets allowed us to identify K and N-derived mitochondrial DNA haplogroups as potential markers of the Neolithic expansion, whose genetic signature would have reached both the Iberian coasts and the Central European plain. Moreover, the observed genetic affinities between the PPNB samples and the modern populations of Cyprus and Crete seem to suggest that the Neolithic was first introduced into Europe through pioneer seafaring colonization.
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Affiliation(s)
- Eva Fernández
- Research Centre in Evolutionary Anthropology and Paleoecology, Liverpool John Moores University, Liverpool, United Kingdom
- Laboratorio de Genética Forense y Genética de Poblaciones, Dpto. Toxicología y Legislación Sanitaria, Facultad de Medicina, Universidad Complutense de Madrid, Madrid, Spain
- * E-mail:
| | - Alejandro Pérez-Pérez
- Dpto. Biología Animal-Unidad de Antropología, Facultad de Biología, Universitat de Barcelona, Barcelona, Spain
| | - Cristina Gamba
- Laboratorio de Genética Forense y Genética de Poblaciones, Dpto. Toxicología y Legislación Sanitaria, Facultad de Medicina, Universidad Complutense de Madrid, Madrid, Spain
| | - Eva Prats
- Centro de Investigación y Desarrollo, Consejo Superior de Investigaciones Científicas, Barcelona, Spain
| | - Pedro Cuesta
- Dpto. de Apoyo a la Investigación, Servicios informáticos de la Universidad Complutense de Madrid, Madrid, Spain
| | - Josep Anfruns
- Dep. Prehistoria, Facultad de Filosofía y Letras, Universitat Autónoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Miquel Molist
- Dep. Prehistoria, Facultad de Filosofía y Letras, Universitat Autónoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Eduardo Arroyo-Pardo
- Laboratorio de Genética Forense y Genética de Poblaciones, Dpto. Toxicología y Legislación Sanitaria, Facultad de Medicina, Universidad Complutense de Madrid, Madrid, Spain
| | - Daniel Turbón
- Dpto. Biología Animal-Unidad de Antropología, Facultad de Biología, Universitat de Barcelona, Barcelona, Spain
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Veeramah KR, Hammer MF. The impact of whole-genome sequencing on the reconstruction of human population history. Nat Rev Genet 2014; 15:149-62. [PMID: 24492235 DOI: 10.1038/nrg3625] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Examining patterns of molecular genetic variation in both modern-day and ancient humans has proved to be a powerful approach to learn about our origins. Rapid advances in DNA sequencing technology have allowed us to characterize increasing amounts of genomic information. Although this clearly provides unprecedented power for inference, it also introduces more complexity into the way we use and interpret such data. Here, we review ongoing debates that have been influenced by improvements in our ability to sequence DNA and discuss some of the analytical challenges that need to be overcome in order to fully exploit the rich historical information that is contained in the entirety of the human genome.
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Affiliation(s)
- Krishna R Veeramah
- 1] Arizona Research Laboratories Division of Biotechnology, Room 231, Life Sciences South, 1007 East Lowell Street, University of Arizona, Tucson, Arizona 85721, USA. [2] Stony Brook University, Stony Brook, New York 11794-5245, USA
| | - Michael F Hammer
- Arizona Research Laboratories Division of Biotechnology, Room 231, Life Sciences South, 1007 East Lowell Street, University of Arizona, Tucson, Arizona 85721, USA
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28
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Sverrisdóttir OÓ, Timpson A, Toombs J, Lecoeur C, Froguel P, Carretero JM, Arsuaga Ferreras JL, Götherström A, Thomas MG. Direct estimates of natural selection in Iberia indicate calcium absorption was not the only driver of lactase persistence in Europe. Mol Biol Evol 2014; 31:975-83. [PMID: 24448642 DOI: 10.1093/molbev/msu049] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Lactase persistence (LP) is a genetically determined trait whereby the enzyme lactase is expressed throughout adult life. Lactase is necessary for the digestion of lactose--the main carbohydrate in milk--and its production is downregulated after the weaning period in most humans and all other mammals studied. Several sources of evidence indicate that LP has evolved independently, in different parts of the world over the last 10,000 years, and has been subject to strong natural selection in dairying populations. In Europeans, LP is strongly associated with, and probably caused by, a single C to T mutation 13,910 bp upstream of the lactase (LCT) gene (-13,910*T). Despite a considerable body of research, the reasons why LP should provide such a strong selective advantage remain poorly understood. In this study, we examine one of the most widely cited hypotheses for selection on LP--that fresh milk consumption supplemented the poor vitamin D and calcium status of northern Europe's early farmers (the calcium assimilation hypothesis). We do this by testing for natural selection on -13,910*T using ancient DNA data from the skeletal remains of eight late Neolithic Iberian individuals, whom we would not expect to have poor vitamin D and calcium status because of relatively high incident UVB light levels. None of the eight samples successfully typed in the study had the derived T-allele. In addition, we reanalyze published data from French Neolithic remains to both test for population continuity and further examine the evolution of LP in the region. Using simulations that accommodate genetic drift, natural selection, uncertainty in calibrated radiocarbon dates, and sampling error, we find that natural selection is still required to explain the observed increase in allele frequency. We conclude that the calcium assimilation hypothesis is insufficient to explain the spread of LP in Europe.
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Affiliation(s)
- Oddny Ósk Sverrisdóttir
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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29
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Brotherton P, Haak W, Templeton J, Brandt G, Soubrier J, Jane Adler C, Richards SM, Der Sarkissian C, Ganslmeier R, Friederich S, Dresely V, van Oven M, Kenyon R, Van der Hoek MB, Korlach J, Luong K, Ho SYW, Quintana-Murci L, Behar DM, Meller H, Alt KW, Cooper A. Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans. Nat Commun 2013; 4:1764. [PMID: 23612305 DOI: 10.1038/ncomms2656] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Accepted: 02/27/2013] [Indexed: 11/09/2022] Open
Abstract
Haplogroup H dominates present-day Western European mitochondrial DNA variability (>40%), yet was less common (~19%) among Early Neolithic farmers (~5450 BC) and virtually absent in Mesolithic hunter-gatherers. Here we investigate this major component of the maternal population history of modern Europeans and sequence 39 complete haplogroup H mitochondrial genomes from ancient human remains. We then compare this 'real-time' genetic data with cultural changes taking place between the Early Neolithic (~5450 BC) and Bronze Age (~2200 BC) in Central Europe. Our results reveal that the current diversity and distribution of haplogroup H were largely established by the Mid Neolithic (~4000 BC), but with substantial genetic contributions from subsequent pan-European cultures such as the Bell Beakers expanding out of Iberia in the Late Neolithic (~2800 BC). Dated haplogroup H genomes allow us to reconstruct the recent evolutionary history of haplogroup H and reveal a mutation rate 45% higher than current estimates for human mitochondria.
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Affiliation(s)
- Paul Brotherton
- The Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia 5005, Australia.,Archaeogenetics Research Group, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK
| | - Wolfgang Haak
- The Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Jennifer Templeton
- The Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Guido Brandt
- Institute of Anthropology, Colonel-Kleinmann Weg 2, Johannes Gutenberg University, Mainz, D-55128 Mainz, Germany
| | - Julien Soubrier
- The Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Christina Jane Adler
- The Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Stephen M Richards
- The Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Clio Der Sarkissian
- The Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Robert Ganslmeier
- State Office for Heritage Management and Archaeology Saxony-Anhalt / State Museum for Prehistory Halle, Richard-Wagner-Straße 9, D-06114 Halle/Saale, Germany
| | - Susanne Friederich
- State Office for Heritage Management and Archaeology Saxony-Anhalt / State Museum for Prehistory Halle, Richard-Wagner-Straße 9, D-06114 Halle/Saale, Germany
| | - Veit Dresely
- State Office for Heritage Management and Archaeology Saxony-Anhalt / State Museum for Prehistory Halle, Richard-Wagner-Straße 9, D-06114 Halle/Saale, Germany
| | - Mannis van Oven
- Department of Forensic Molecular Biology, Erasmus MC, University Medical Centre, Rotterdam, 3000 CA Rotterdam, The Netherlands
| | | | | | | | | | - Simon Y W Ho
- School of Biological Sciences, The University of Sydney, New South Wales 2006, Australia
| | | | | | - Harald Meller
- State Office for Heritage Management and Archaeology Saxony-Anhalt / State Museum for Prehistory Halle, Richard-Wagner-Straße 9, D-06114 Halle/Saale, Germany
| | - Kurt W Alt
- Institute of Anthropology, Colonel-Kleinmann Weg 2, Johannes Gutenberg University, Mainz, D-55128 Mainz, Germany
| | - Alan Cooper
- Institute of Anthropology, Colonel-Kleinmann Weg 2, Johannes Gutenberg University, Mainz, D-55128 Mainz, Germany
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30
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Olivieri A, Pala M, Gandini F, Hooshiar Kashani B, Perego UA, Woodward SR, Grugni V, Battaglia V, Semino O, Achilli A, Richards MB, Torroni A. Mitogenomes from two uncommon haplogroups mark late glacial/postglacial expansions from the near east and neolithic dispersals within Europe. PLoS One 2013; 8:e70492. [PMID: 23936216 PMCID: PMC3729697 DOI: 10.1371/journal.pone.0070492] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 06/20/2013] [Indexed: 11/19/2022] Open
Abstract
The current human mitochondrial (mtDNA) phylogeny does not equally represent all human populations but is biased in favour of representatives originally from north and central Europe. This especially affects the phylogeny of some uncommon West Eurasian haplogroups, including I and W, whose southern European and Near Eastern components are very poorly represented, suggesting that extensive hidden phylogenetic substructure remains to be uncovered. This study expanded and re-analysed the available datasets of I and W complete mtDNA genomes, reaching a comprehensive 419 mitogenomes, and searched for precise correlations between the ages and geographical distributions of their numerous newly identified subclades with events of human dispersal which contributed to the genetic formation of modern Europeans. Our results showed that haplogroups I (within N1a1b) and W originated in the Near East during the Last Glacial Maximum or pre-warming period (the period of gradual warming between the end of the LGM, ∼19 ky ago, and the beginning of the first main warming phase, ∼15 ky ago) and, like the much more common haplogroups J and T, may have been involved in Late Glacial expansions starting from the Near East. Thus our data contribute to a better definition of the Late and postglacial re-peopling of Europe, providing further evidence for the scenario that major population expansions started after the Last Glacial Maximum but before Neolithic times, but also evidencing traces of diffusion events in several I and W subclades dating to the European Neolithic and restricted to Europe.
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Affiliation(s)
- Anna Olivieri
- Dipartimento di Biologia e Biotecnologie L. Spallanzani, Università di Pavia, Pavia, Italy.
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31
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Lacan M, Keyser C, Crubézy E, Ludes B. Ancestry of modern Europeans: contributions of ancient DNA. Cell Mol Life Sci 2013; 70:2473-87. [PMID: 23052219 PMCID: PMC11113793 DOI: 10.1007/s00018-012-1180-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 09/21/2012] [Accepted: 09/24/2012] [Indexed: 12/25/2022]
Abstract
Understanding the peopling history of Europe is crucial to comprehend the origins of modern populations. Of course, the analysis of current genetic data offers several explanations about human migration patterns which occurred on this continent, but it fails to explain precisely the impact of each demographic event. In this context, direct access to the DNA of ancient specimens allows the overcoming of recent demographic phenomena, which probably highly modified the constitution of the current European gene pool. In recent years, several DNA studies have been successfully conducted from ancient human remains thanks to the improvement of molecular techniques. They have brought new fundamental information on the peopling of Europe and allowed us to refine our understanding of European prehistory. In this review, we will detail all the ancient DNA studies performed to date on ancient European DNA from the Middle Paleolithic to the beginning of the protohistoric period.
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Affiliation(s)
- Marie Lacan
- Laboratoire AMIS, CNRS UMR 5288, 37 Allées Jules Guesde,Toulouse cedex 3, France.
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32
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Der Sarkissian C, Balanovsky O, Brandt G, Khartanovich V, Buzhilova A, Koshel S, Zaporozhchenko V, Gronenborn D, Moiseyev V, Kolpakov E, Shumkin V, Alt KW, Balanovska E, Cooper A, Haak W. Ancient DNA reveals prehistoric gene-flow from siberia in the complex human population history of North East Europe. PLoS Genet 2013; 9:e1003296. [PMID: 23459685 PMCID: PMC3573127 DOI: 10.1371/journal.pgen.1003296] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 12/18/2012] [Indexed: 11/25/2022] Open
Abstract
North East Europe harbors a high diversity of cultures and languages, suggesting a complex genetic history. Archaeological, anthropological, and genetic research has revealed a series of influences from Western and Eastern Eurasia in the past. While genetic data from modern-day populations is commonly used to make inferences about their origins and past migrations, ancient DNA provides a powerful test of such hypotheses by giving a snapshot of the past genetic diversity. In order to better understand the dynamics that have shaped the gene pool of North East Europeans, we generated and analyzed 34 mitochondrial genotypes from the skeletal remains of three archaeological sites in northwest Russia. These sites were dated to the Mesolithic and the Early Metal Age (7,500 and 3,500 uncalibrated years Before Present). We applied a suite of population genetic analyses (principal component analysis, genetic distance mapping, haplotype sharing analyses) and compared past demographic models through coalescent simulations using Bayesian Serial SimCoal and Approximate Bayesian Computation. Comparisons of genetic data from ancient and modern-day populations revealed significant changes in the mitochondrial makeup of North East Europeans through time. Mesolithic foragers showed high frequencies and diversity of haplogroups U (U2e, U4, U5a), a pattern observed previously in European hunter-gatherers from Iberia to Scandinavia. In contrast, the presence of mitochondrial DNA haplogroups C, D, and Z in Early Metal Age individuals suggested discontinuity with Mesolithic hunter-gatherers and genetic influx from central/eastern Siberia. We identified remarkable genetic dissimilarities between prehistoric and modern-day North East Europeans/Saami, which suggests an important role of post-Mesolithic migrations from Western Europe and subsequent population replacement/extinctions. This work demonstrates how ancient DNA can improve our understanding of human population movements across Eurasia. It contributes to the description of the spatio-temporal distribution of mitochondrial diversity and will be of significance for future reconstructions of the history of Europeans. The history of human populations can be retraced by studying the archaeological and anthropological record, but also by examining the current distribution of genetic markers, such as the maternally inherited mitochondrial DNA. Ancient DNA research allows the retrieval of DNA from ancient skeletal remains and contributes to the reconstruction of the human population history through the comparison of ancient and present-day genetic data. Here, we analysed the mitochondrial DNA of prehistoric remains from archaeological sites dated to 7,500 and 3,500 years Before Present. These sites are located in North East Europe, a region that displays a significant cultural and linguistic diversity today but for which no ancient human DNA was available before. We show that prehistoric hunter-gatherers of North East Europe were genetically similar to other European foragers. We also detected a prehistoric genetic input from Siberia, followed by migrations from Western Europe into North East Europe. Our research contributes to the understanding of the origins and past dynamics of human population in Europe.
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Affiliation(s)
- Clio Der Sarkissian
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia
- * E-mail:
| | - Oleg Balanovsky
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, Russia
- Vavilov Institute for General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Guido Brandt
- Institute of Anthropology, Johannes Gutenberg University of Mainz, Mainz, Germany
| | | | | | - Sergey Koshel
- Faculty of Geography, Moscow State University, Moscow, Russia
| | - Valery Zaporozhchenko
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, Russia
| | | | | | - Eugen Kolpakov
- Institute for the History of Material Culture, Russian Academy of Science, St. Petersburg, Russia
| | - Vladimir Shumkin
- Institute for the History of Material Culture, Russian Academy of Science, St. Petersburg, Russia
| | - Kurt W. Alt
- Institute of Anthropology, Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Elena Balanovska
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, Russia
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Wolfgang Haak
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia
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33
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Origin and diet of the prehistoric hunter-gatherers on the mediterranean island of Favignana (Ègadi Islands, Sicily). PLoS One 2012; 7:e49802. [PMID: 23209602 PMCID: PMC3509116 DOI: 10.1371/journal.pone.0049802] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 10/16/2012] [Indexed: 11/19/2022] Open
Abstract
Hunter-gatherers living in Europe during the transition from the late Pleistocene to the Holocene intensified food acquisition by broadening the range of resources exploited to include marine taxa. However, little is known on the nature of this dietary change in the Mediterranean Basin. A key area to investigate this issue is the archipelago of the Ègadi Islands, most of which were connected to Sicily until the early Holocene. The site of Grotta d’Oriente, on the present-day island of Favignana, was occupied by hunter-gatherers when Postglacial environmental changes were taking place (14,000-7,500 cal BP). Here we present the results of AMS radiocarbon dating, palaeogenetic and isotopic analyses undertaken on skeletal remains of the humans buried at Grotta d’Oriente. Analyses of the mitochondrial hypervariable first region of individual Oriente B, which belongs to the HV-1 haplogroup, suggest for the first time on genetic grounds that humans living in Sicily during the early Holocene could have originated from groups that migrated from the Italian Peninsula around the Last Glacial Maximum. Carbon and nitrogen isotope analyses show that the Upper Palaeolithic and Mesolithic hunter-gatherers of Favignana consumed almost exclusively protein from terrestrial game and that there was only a slight increase in marine food consumption from the late Pleistocene to the early Holocene. This dietary change was similar in scale to that at sites on mainland Sicily and in the rest of the Mediterranean, suggesting that the hunter-gatherers of Grotta d’Oriente did not modify their subsistence strategies specifically to adapt to the progressive isolation of Favignana. The limited development of technologies for intensively exploiting marine resources was probably a consequence both of Mediterranean oligotrophy and of the small effective population size of these increasingly isolated human groups, which made innovation less likely and prevented transmission of fitness-enhancing adaptations.
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Abstract
Paleopopulation genetics is a new field that focuses on the population genetics of extinct groups and ancestral populations (i.e., populations ancestral to extant groups). With recent advances in DNA sequencing technologies, we now have unprecedented ability to directly assay genetic variation from fossils. This allows us to address issues, such as past population structure, changes in population size, and evolutionary relationships between taxa, at a much greater resolution than can traditional population genetics studies. In this review, we discuss recent developments in this emerging field as well as prospects for the future.
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Affiliation(s)
- Jeffrey D Wall
- Institute for Human Genetics and Department of Epidemiology and Biostatistics, University of California, San Francisco, California 94134, USA.
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35
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Pinhasi R, Thomas MG, Hofreiter M, Currat M, Burger J. The genetic history of Europeans. Trends Genet 2012; 28:496-505. [PMID: 22889475 DOI: 10.1016/j.tig.2012.06.006] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Revised: 06/16/2012] [Accepted: 06/22/2012] [Indexed: 10/28/2022]
Abstract
The evolutionary history of modern humans is characterized by numerous migrations driven by environmental change, population pressures, and cultural innovations. In Europe, the events most widely considered to have had a major impact on patterns of genetic diversity are the initial colonization of the continent by anatomically modern humans (AMH), the last glacial maximum, and the Neolithic transition. For some decades it was assumed that the geographical structuring of genetic diversity within Europe was mainly the result of gene flow during and soon after the Neolithic transition, but recent advances in next-generation sequencing (NGS) technologies, computer simulation modeling, and ancient DNA (aDNA) analyses are challenging this simplistic view. Here we review the current knowledge on the evolutionary history of humans in Europe based on archaeological and genetic data.
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Affiliation(s)
- Ron Pinhasi
- Department of Archaeology, University College Cork, Cork, Ireland.
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36
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37
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Pinhasi R, von Cramon-Taubadel N. A craniometric perspective on the transition to agriculture in Europe. Hum Biol 2012; 84:45-66. [PMID: 22452428 DOI: 10.3378/027.084.0102] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Debates surrounding the nature of the Neolithic demographic transition in Europe have historically centered on two opposing models: a "demic" diffusion model whereby incoming farmers from the Near East and Anatolia effectively replaced or completely assimilated indigenous Mesolithic foraging communities, and an "indigenist" model resting on the assumption that ideas relating to agriculture and animal domestication diffused from the Near East but with little or no gene flow. The extreme versions of these dichotomous models were heavily contested primarily on the basis of archeological and modern genetic data. However, in recent years a growing acceptance has arisen of the likelihood that both processes were ongoing throughout the Neolithic transition and that a more complex, regional approach is required to fully understand the change from a foraging to a primarily agricultural mode of subsistence in Europe. Craniometric data were particularly useful for testing these more complex scenarios, as they can reliably be employed as a proxy for the genetic relationships among Mesolithic and Neolithic populations. In contrast, modern genetic data assume that modern European populations accurately reflect the genetic structure of Europe at the time of the Neolithic transition, while ancient DNA data are still not geographically or temporally detailed enough to test continent-wide processes. Here, with particular emphasis on the role of craniometric analyses, we review the current state of knowledge regarding the cultural and biological nature of the Neolithic transition in Europe.
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Affiliation(s)
- Ron Pinhasi
- Department of Archaeology, University College Cork, Cork, Ireland.
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38
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Sánchez-Quinto F, Schroeder H, Ramirez O, Avila-Arcos MC, Pybus M, Olalde I, Velazquez AMV, Marcos MEP, Encinas JMV, Bertranpetit J, Orlando L, Gilbert MTP, Lalueza-Fox C. Genomic affinities of two 7,000-year-old Iberian hunter-gatherers. Curr Biol 2012; 22:1494-9. [PMID: 22748318 DOI: 10.1016/j.cub.2012.06.005] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Revised: 05/08/2012] [Accepted: 06/04/2012] [Indexed: 10/28/2022]
Abstract
The genetic background of the European Mesolithic and the extent of population replacement during the Neolithic is poorly understood, both due to the scarcity of human remains from that period and the inherent methodological difficulties of ancient DNA research. However, advances in sequencing technologies are both increasing data yields and providing supporting evidence for data authenticity, such as nucleotide misincorporation patterns. We use these methods to characterize both the mitochondrial DNA genome and generate shotgun genomic data from two exceptionally well-preserved 7,000-year-old Mesolithic individuals from La Braña-Arintero site in León (Northwestern Spain). The mitochondria of both individuals are assigned to U5b2c1, a haplotype common among the small number of other previously studied Mesolithic individuals from Northern and Central Europe. This suggests a remarkable genetic uniformity and little phylogeographic structure over a large geographic area of the pre-Neolithic populations. Using Approximate Bayesian Computation, a model of genetic continuity from Mesolithic to Neolithic populations is poorly supported. Furthermore, analyses of 1.34% and 0.53% of their nuclear genomes, containing about 50,000 and 20,000 ancestry informative SNPs, respectively, show that these two Mesolithic individuals are not related to current populations from either the Iberian Peninsula or Southern Europe.
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Nikitin AG, Newton JR, Potekhina ID. Mitochondrial haplogroup C in ancient mitochondrial DNA from Ukraine extends the presence of East Eurasian genetic lineages in Neolithic Central and Eastern Europe. J Hum Genet 2012; 57:610-2. [PMID: 22673688 DOI: 10.1038/jhg.2012.69] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Recent studies of ancient mitochondrial DNA (mtDNA) lineages have revealed the presence of East Eurasian mtDNA haplogroups in the Central European Neolithic. Here we report the finding of East Eurasian lineages in ancient mtDNA from two Neolithic cemeteries of the North Pontic Region (NPR) in Ukraine. In our study, comprehensive haplotyping information was obtained for 7 out of 18 specimens. Although the majority of identified mtDNA haplogroups belonged to the traditional West Eurasian lineages of H and U, three specimens were determined to belong to the lineages of mtDNA haplogroup C. This find extends the presence of East Eurasian lineages in Neolithic Europe from the Carpathian Mountains to the northern shores of the Black Sea and provides the first genetic account of Neolithic mtDNA lineages from the NPR.
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Affiliation(s)
- Alexey G Nikitin
- Biology Department, Grand Valley State University, Allendale, MI 49401, USA.
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Pala M, Olivieri A, Achilli A, Accetturo M, Metspalu E, Reidla M, Tamm E, Karmin M, Reisberg T, Kashani B, Perego U, Carossa V, Gandini F, Pereira J, Soares P, Angerhofer N, Rychkov S, Al-Zahery N, Carelli V, Sanati M, Houshmand M, Hatina J, Macaulay V, Pereira L, Woodward S, Davies W, Gamble C, Baird D, Semino O, Villems R, Torroni A, Richards M. Mitochondrial DNA signals of late glacial recolonization of Europe from near eastern refugia. Am J Hum Genet 2012; 90:915-24. [PMID: 22560092 DOI: 10.1016/j.ajhg.2012.04.003] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Revised: 03/22/2012] [Accepted: 04/03/2012] [Indexed: 10/28/2022] Open
Abstract
Human populations, along with those of many other species, are thought to have contracted into a number of refuge areas at the height of the last Ice Age. European populations are believed to be, to a large extent, the descendants of the inhabitants of these refugia, and some extant mtDNA lineages can be traced to refugia in Franco-Cantabria (haplogroups H1, H3, V, and U5b1), the Italian Peninsula (U5b3), and the East European Plain (U4 and U5a). Parts of the Near East, such as the Levant, were also continuously inhabited throughout the Last Glacial Maximum, but unlike western and eastern Europe, no archaeological or genetic evidence for Late Glacial expansions into Europe from the Near East has hitherto been discovered. Here we report, on the basis of an enlarged whole-genome mitochondrial database, that a substantial, perhaps predominant, signal from mitochondrial haplogroups J and T, previously thought to have spread primarily from the Near East into Europe with the Neolithic population, may in fact reflect dispersals during the Late Glacial period, ∼19-12 thousand years (ka) ago.
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Lee EJ, Makarewicz C, Renneberg R, Harder M, Krause-Kyora B, Müller S, Ostritz S, Fehren-Schmitz L, Schreiber S, Müller J, von Wurmb-Schwark N, Nebel A. Emerging genetic patterns of the European Neolithic: perspectives from a late Neolithic Bell Beaker burial site in Germany. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2012; 148:571-9. [PMID: 22552938 DOI: 10.1002/ajpa.22074] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Revised: 03/08/2012] [Accepted: 03/12/2012] [Indexed: 11/05/2022]
Abstract
The transition from hunting and gathering to agriculture in Europe is associated with demographic changes that may have shifted the human gene pool of the region as a result of an influx of Neolithic farmers from the Near East. However, the genetic composition of populations after the earliest Neolithic, when a diverse mosaic of societies that had been fully engaged in agriculture for some time appeared in central Europe, is poorly known. At this period during the Late Neolithic (ca. 2,800-2,000 BC), regionally distinctive burial patterns associated with two different cultural groups emerge, Bell Beaker and Corded Ware, and may reflect differences in how these societies were organized. Ancient DNA analyses of human remains from the Late Neolithic Bell Beaker site of Kromsdorf, Germany showed distinct mitochondrial haplotypes for six individuals, which were classified under the haplogroups I1, K1, T1, U2, U5, and W5, and two males were identified as belonging to the Y haplogroup R1b. In contrast to other Late Neolithic societies in Europe emphasizing maintenance of biological relatedness in mortuary contexts, the diversity of maternal haplotypes evident at Kromsdorf suggests that burial practices of Bell Beaker communities operated outside of social norms based on shared maternal lineages. Furthermore, our data, along with those from previous studies, indicate that modern U5-lineages may have received little, if any, contribution from the Mesolithic or Neolithic mitochondrial gene pool.
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Affiliation(s)
- Esther J Lee
- Graduate School "Human Development in Landscapes," Christian-Albrechts-University of Kiel, Germany
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Regueiro M, Rivera L, Damnjanovic T, Lukovic L, Milasin J, Herrera RJ. High levels of Paleolithic Y-chromosome lineages characterize Serbia. Gene 2012; 498:59-67. [PMID: 22310393 DOI: 10.1016/j.gene.2012.01.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Accepted: 01/19/2012] [Indexed: 10/14/2022]
Abstract
Whether present-day European genetic variation and its distribution patterns can be attributed primarily to the initial peopling of Europe by anatomically modern humans during the Paleolithic, or to latter Near Eastern Neolithic input is still the subject of debate. Southeastern Europe has been a crossroads for several cultures since Paleolithic times and the Balkans, specifically, would have been part of the route used by Neolithic farmers to enter Europe. Given its geographic location in the heart of the Balkan Peninsula at the intersection of Central and Southeastern Europe, Serbia represents a key geographical location that may provide insight to elucidate the interactions between indigenous Paleolithic people and agricultural colonists from the Fertile Crescent. In this study, we examine, for the first time, the Y-chromosome constitution of the general Serbian population. A total of 103 individuals were sampled and their DNA analyzed for 104 Y-chromosome bi-allelic markers and 17 associated STR loci. Our results indicate that approximately 58% of Serbian Y-chromosomes (I1-M253, I2a-P37.2 and R1a1a-M198) belong to lineages believed to be pre-Neolithic. On the other hand, the signature of putative Near Eastern Neolithic lineages, including E1b1b1a1-M78, G2a-P15, J1-M267, J2-M172 and R1b1a2-M269 accounts for 39% of the Y-chromosome. Haplogroup frequency distributions in Western and Eastern Europe reveal a spotted landscape of paleolithic Y chromosomes, undermining continental-wide generalizations. Furthermore, an examination of the distribution of Y-chromosome filiations in Europe indicates extreme levels of Paleolithic lineages in a region encompassing Serbia, Bosnia-Herzegovina and Croatia, possibly the result of Neolithic migrations encroaching on Paleolithic populations against the Adriatic Sea.
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Affiliation(s)
- Maria Regueiro
- Department of Molecular and Human Genetics, College of Medicine, Florida International University, Miami, FL 33199, USA
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Hervella M, Izagirre N, Alonso S, Fregel R, Alonso A, Cabrera VM, de la Rúa C. Ancient DNA from hunter-gatherer and farmer groups from Northern Spain supports a random dispersion model for the Neolithic expansion into Europe. PLoS One 2012; 7:e34417. [PMID: 22563371 PMCID: PMC3340892 DOI: 10.1371/journal.pone.0034417] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 02/28/2012] [Indexed: 11/25/2022] Open
Abstract
Background/Principal Findings The phenomenon of Neolithisation refers to the transition of prehistoric
populations from a hunter-gatherer to an agro-pastoralist lifestyle.
Traditionally, the spread of an agro-pastoralist economy into Europe has
been framed within a dichotomy based either on an acculturation phenomenon
or on a demic diffusion. However, the nature and speed of this transition is
a matter of continuing scientific debate in archaeology, anthropology, and
human population genetics. In the present study, we have analyzed the
mitochondrial DNA diversity in hunter-gatherers and first farmers from
Northern Spain, in relation to the debate surrounding the phenomenon of
Neolithisation in Europe. Methodology/Significance Analysis of mitochondrial DNA was carried out on 54 individuals from Upper
Paleolithic and Early Neolithic, which were recovered from nine
archaeological sites from Northern Spain (Basque Country, Navarre and
Cantabria). In addition, to take all necessary precautions to avoid
contamination, different authentication criteria were applied in this study,
including: DNA quantification, cloning, duplication (51% of the
samples) and replication of the results (43% of the samples) by two
independent laboratories. Statistical and multivariate analyses of the
mitochondrial variability suggest that the genetic influence of
Neolithisation did not spread uniformly throughout Europe, producing
heterogeneous genetic consequences in different geographical regions,
rejecting the traditional models that explain the Neolithisation in
Europe. Conclusion The differences detected in the mitochondrial DNA lineages of Neolithic
groups studied so far (including these ones of this study) suggest different
genetic impact of Neolithic in Central Europe, Mediterranean Europe and the
Cantabrian fringe. The genetic data obtained in this study provide support
for a random dispersion model for Neolithic farmers. This random dispersion
had a different impact on the various geographic regions, and thus
contradicts the more simplistic total acculturation and replacement models
proposed so far to explain Neolithisation.
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Affiliation(s)
- Montserrat Hervella
- Department of Genetics, Physical Anthropology
and Animal Physiology, University of the Basque Country, Bizkaia,
Spain
| | - Neskuts Izagirre
- Department of Genetics, Physical Anthropology
and Animal Physiology, University of the Basque Country, Bizkaia,
Spain
| | - Santos Alonso
- Department of Genetics, Physical Anthropology
and Animal Physiology, University of the Basque Country, Bizkaia,
Spain
| | - Rosa Fregel
- Department of Genetics, University of La
Laguna, La Laguna, Santa Cruz de Tenerife, Spain
| | - Antonio Alonso
- Department of Biology, National Institute of
Toxicology and Forensic Sciences, Madrid, Spain
| | - Vicente M. Cabrera
- Department of Genetics, University of La
Laguna, La Laguna, Santa Cruz de Tenerife, Spain
| | - Concepción de la Rúa
- Department of Genetics, Physical Anthropology
and Animal Physiology, University of the Basque Country, Bizkaia,
Spain
- * E-mail:
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Fu Q, Rudan P, Pääbo S, Krause J. Complete mitochondrial genomes reveal neolithic expansion into Europe. PLoS One 2012; 7:e32473. [PMID: 22427842 PMCID: PMC3302788 DOI: 10.1371/journal.pone.0032473] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 01/31/2012] [Indexed: 11/18/2022] Open
Abstract
The Neolithic transition from hunting and gathering to farming and cattle breeding marks one of the most drastic cultural changes in European prehistory. Short stretches of ancient mitochondrial DNA (mtDNA) from skeletons of pre-Neolithic hunter-gatherers as well as early Neolithic farmers support the demic diffusion model where a migration of early farmers from the Near East and a replacement of pre-Neolithic hunter-gatherers are largely responsible for cultural innovation and changes in subsistence strategies during the Neolithic revolution in Europe. In order to test if a signal of population expansion is still present in modern European mitochondrial DNA, we analyzed a comprehensive dataset of 1,151 complete mtDNAs from present-day Europeans. Relying upon ancient DNA data from previous investigations, we identified mtDNA haplogroups that are typical for early farmers and hunter-gatherers, namely H and U respectively. Bayesian skyline coalescence estimates were then used on subsets of complete mtDNAs from modern populations to look for signals of past population expansions. Our analyses revealed a population expansion between 15,000 and 10,000 years before present (YBP) in mtDNAs typical for hunters and gatherers, with a decline between 10,000 and 5,000 YBP. These corresponded to an analogous population increase approximately 9,000 YBP for mtDNAs typical of early farmers. The observed changes over time suggest that the spread of agriculture in Europe involved the expansion of farming populations into Europe followed by the eventual assimilation of resident hunter-gatherers. Our data show that contemporary mtDNA datasets can be used to study ancient population history if only limited ancient genetic data is available.
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Affiliation(s)
- Qiaomei Fu
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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Kirsanow K, Burger J. Ancient human DNA. Ann Anat 2012; 194:121-32. [PMID: 22169595 DOI: 10.1016/j.aanat.2011.11.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Revised: 11/07/2011] [Accepted: 11/08/2011] [Indexed: 12/11/2022]
Abstract
The contribution of palaeogenetic data to the study of various aspects of hominin biology and evolution has been significant, and has the potential to increase substantially with the widespread implementation of next generation sequencing techniques. Here we discuss the present state-of-the-art of ancient human DNA analysis and the characteristics of hominin aDNA that make sequence validation particularly complex. A brief overview of the development of anthropological palaeogenetic analysis is given to illustrate the technical challenges motivating recent technological advancements.
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Affiliation(s)
- Karola Kirsanow
- Johannes Gutenberg-University Mainz, Institute of Anthropology, Germany
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Gamba C, Fernández E, Tirado M, Deguilloux MF, Pemonge MH, Utrilla P, Edo M, Molist M, Rasteiro R, Chikhi L, Arroyo-Pardo E. Ancient DNA from an Early Neolithic Iberian population supports a pioneer colonization by first farmers. Mol Ecol 2011; 21:45-56. [PMID: 22117930 DOI: 10.1111/j.1365-294x.2011.05361.x] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Neolithic transition has been widely debated particularly regarding the extent to which this revolution implied a demographic expansion from the Near East. We attempted to shed some light on this process in northeastern Iberia by combining ancient DNA (aDNA) data from Early Neolithic settlers and published DNA data from Middle Neolithic and modern samples from the same region. We successfully extracted and amplified mitochondrial DNA from 13 human specimens, found at three archaeological sites dated back to the Cardial culture in the Early Neolithic (Can Sadurní and Chaves) and to the Late Early Neolithic (Sant Pau del Camp). We found that haplogroups with a low frequency in modern populations-N* and X1-are found at higher frequencies in our Early Neolithic population (∼31%). Genetic differentiation between Early and Middle Neolithic populations was significant (F(ST) ∼0.13, P<10(-5)), suggesting that genetic drift played an important role at this time. To improve our understanding of the Neolithic demographic processes, we used a Bayesian coalescence-based simulation approach to identify the most likely of three demographic scenarios that might explain the genetic data. The three scenarios were chosen to reflect archaeological knowledge and previous genetic studies using similar inferential approaches. We found that models that ignore population structure, as previously used in aDNA studies, are unlikely to explain the data. Our results are compatible with a pioneer colonization of northeastern Iberia at the Early Neolithic characterized by the arrival of small genetically distinctive groups, showing cultural and genetic connections with the Near East.
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Affiliation(s)
- C Gamba
- Laboratorio de Genética Forense y Genética de Poblaciones, Facultad de Medicina, Pabellón 7, 4ª Planta, Universidad Complutense de Madrid, Avenida Complutense s/n, 28040 Madrid, Spain.
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Ancient DNA suggests the leading role played by men in the Neolithic dissemination. Proc Natl Acad Sci U S A 2011; 108:18255-9. [PMID: 22042855 DOI: 10.1073/pnas.1113061108] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The impact of the Neolithic dispersal on the western European populations is subject to continuing debate. To trace and date genetic lineages potentially brought during this transition and so understand the origin of the gene pool of current populations, we studied DNA extracted from human remains excavated in a Spanish funeral cave dating from the beginning of the fifth millennium B.C. Thanks to a "multimarkers" approach based on the analysis of mitochondrial and nuclear DNA (autosomes and Y-chromosome), we obtained information on the early Neolithic funeral practices and on the biogeographical origin of the inhumed individuals. No close kinship was detected. Maternal haplogroups found are consistent with pre-Neolithic settlement, whereas the Y-chromosomal analyses permitted confirmation of the existence in Spain approximately 7,000 y ago of two haplogroups previously associated with the Neolithic transition: G2a and E1b1b1a1b. These results are highly consistent with those previously found in Neolithic individuals from French Late Neolithic individuals, indicating a surprising temporal genetic homogeneity in these groups. The high frequency of G2a in Neolithic samples in western Europe could suggest, furthermore, that the role of men during Neolithic dispersal could be greater than currently estimated.
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Simón M, Jordana X, Armentano N, Santos C, Díaz N, Solórzano E, López JB, González-Ruiz M, Malgosa A. The presence of nuclear families in prehistoric collective burials revisited: The bronze age burial of montanissell cave (Spain) in the light of aDNA. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2011; 146:406-13. [DOI: 10.1002/ajpa.21590] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Accepted: 06/29/2011] [Indexed: 11/07/2022]
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Guba Z, Hadadi É, Major Á, Furka T, Juhász E, Koós J, Nagy K, Zeke T. HVS-I polymorphism screening of ancient human mitochondrial DNA provides evidence for N9a discontinuity and East Asian haplogroups in the Neolithic Hungary. J Hum Genet 2011; 56:784-96. [DOI: 10.1038/jhg.2011.103] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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50
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García-Garcerà M, Gigli E, Sanchez-Quinto F, Ramirez O, Calafell F, Civit S, Lalueza-Fox C. Fragmentation of contaminant and endogenous DNA in ancient samples determined by shotgun sequencing; prospects for human palaeogenomics. PLoS One 2011; 6:e24161. [PMID: 21904610 PMCID: PMC3164143 DOI: 10.1371/journal.pone.0024161] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 08/01/2011] [Indexed: 12/20/2022] Open
Abstract
Background Despite the successful retrieval of genomes from past remains, the prospects for human palaeogenomics remain unclear because of the difficulty of distinguishing contaminant from endogenous DNA sequences. Previous sequence data generated on high-throughput sequencing platforms indicate that fragmentation of ancient DNA sequences is a characteristic trait primarily arising due to depurination processes that create abasic sites leading to DNA breaks. Methodology/Principals Findings To investigate whether this pattern is present in ancient remains from a temperate environment, we have 454-FLX pyrosequenced different samples dated between 5,500 and 49,000 years ago: a bone from an extinct goat (Myotragus balearicus) that was treated with a depurinating agent (bleach), an Iberian lynx bone not subjected to any treatment, a human Neolithic sample from Barcelona (Spain), and a Neandertal sample from the El Sidrón site (Asturias, Spain). The efficiency of retrieval of endogenous sequences is below 1% in all cases. We have used the non-human samples to identify human sequences (0.35 and 1.4%, respectively), that we positively know are contaminants. Conclusions We observed that bleach treatment appears to create a depurination-associated fragmentation pattern in resulting contaminant sequences that is indistinguishable from previously described endogenous sequences. Furthermore, the nucleotide composition pattern observed in 5′ and 3′ ends of contaminant sequences is much more complex than the flat pattern previously described in some Neandertal contaminants. Although much research on samples with known contaminant histories is needed, our results suggest that endogenous and contaminant sequences cannot be distinguished by the fragmentation pattern alone.
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Affiliation(s)
| | - Elena Gigli
- Institut de Biologia Evolutiva, CSIC-UPF, Barcelona, Spain
| | | | - Oscar Ramirez
- Institut de Biologia Evolutiva, CSIC-UPF, Barcelona, Spain
| | | | - Sergi Civit
- Department de Bioestadística, Universitat de Barcelona, Barcelona, Spain
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